Re: [gmx-users] Trouble running 4.6.4. on cpu+gpu but not on gpu alone
Hi, start with using as many MPI processes as you have GPUs. GROMACS will use several OpenMP threads per MPI process to use all your CPU cores. You can also do that manually with mpirun -np 2 mdrun-mpi -ntomp 6 Carsten On 12/10/2013 10:30 AM, rajat desikan wrote: Dear all, I recently installed gromacs 4.6.4 on our cluster. The configuration is 12 cpus and 2 gpus per node. The build details are given below. I am able to run gromacs on the 2 gpus alone. However, running a job with cpu+gpu fails with a fatal error (given below). Gromacs build: cmake .. -DGMX_CPU_ACCELERATION=SSE2 -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/ *Job1) Pure GPUs:Running* node=1:gpus=2 mpirun –np 2 mdrun-mpi ./ running on 2 GPU cards of the same node. *Job2) CPU+GPUs:Crashed* node=1:ppn=10:gpus=2 mpirun –np 12 mdrun-mpi FATAL error “Using 12 MPI processes Using 2 OpenMP threads per MPI process Compiled acceleration: SSE2 (Gromacs could use SSE4.1 on this machine, which is better) 2 GPUs detected on host cn1.local: #0: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA Tesla M2090, compute cap.: 2.0, ECC: no, stat: compatible 2 GPUs auto-selected for this run. Mapping of GPUs to the 12 PP ranks in this node: #0, #1 --- Program mdrun_mpi, VERSION 4.6.4 Source code file: /home/rajat/softback/gromacs-4.6.4/src/gmxlib/gmx_detect_hardware.c, line: 372 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 12 PP MPI processes per node, but only 2 GPUs were detected. For more information and tips for troubleshooting, please check the GROMACS” -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] deformation in cnt
If the system does not explode, everything is correct. Though your solution is perhaps in the wrong place in relation to the tube. Dr. Vitaly V. Chaban On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Justin Based on your suggestion, I added C-C bond length to z dimension of box (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). Then I used genion to neutralize system using replacing 2 water molecules by 2 Na ions, gro file obtained from genion is strange. When I see this gro file by vmd, some carbon atoms of CNT leave the box. Figure is in the bellow link: https://www.dropbox.com/s/kt1xk4ps3kbxze3/cnt-pic.docx What is reason of this issue? How to fix it? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] what is the mean sar, st, pi, gar and hct of gbsa.itp?
Dear All. Hi. I'm want calculation of dimer protein. My proteins have manganese. But don't have gbsa.itp of manganese. I'm insert Mn data, but I don't know 'sar, st, pi ...' What is the values mean? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/what-is-the-mean-sar-st-pi-gar-and-hct-of-gbsa-itp-tp5013242.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ligand covalently bond with the protein
Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] what is the mean sar, st, pi, gar and hct of gbsa.itp?
On Tue, Dec 10, 2013 at 8:11 AM, C.H. Kim poc...@icloud.com wrote: Dear All. Hi. I'm want calculation of dimer protein. My proteins have manganese. But don't have gbsa.itp of manganese. I'm insert Mn data, but I don't know 'sar, st, pi ...' What is the values mean? Please read manual section 5.3.5 and associated references. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand covalently bond with the protein
On Tue, Dec 10, 2013 at 7:54 AM, aixintiankong aixintiank...@126.comwrote: Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] why it is symmetric
On Mon, Dec 9, 2013 at 12:58 PM, Albert mailmd2...@gmail.com wrote: Hello: I am calculating the water density inside my membrane protein along Z directions. I used the a_ri3DC tool in Gridcount which is a patch in Gromacs for calculation: a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp xyp.dat -xzp xzp.dat -yzp yzp.dat -rzp rzp.dat -rdf rdf.xvg -zdf zdf.xvg -lzdf lzdf.xvg -hxyp hxyp.dat -hrzp hrzp.dat -hrdf hrdf.xvg -dump gridasc.dat Then I plot the water density with above generated file: hrzp.dat I found that the water density along X direction is symmetric even my protein is not symmetric. The water density along Z directions seems to be good. Does anybody have any idea what's problem? Why the density in X direction is symmetric? Why shouldn't it be? Is the density along y symmetric, as well? I have never used a_ri3Dc so I don't know what it's doing, what data you're providing it, or what you should expect, but intuitively, unless a membrane protein protrudes extensively into the aqueous layer, you are not going to see any effect on the water density in x or y. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] OPLS force field issue
On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi es...@sfu.ca wrote: Thanks Justin. I added the bond description in the ffbonded.itp but it does not show in the topol.top file. In ffbonded.itp we have: [ bondtypes ] ; ij func b0 kb OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98 OWLP 10.01750 753120.0 ; -idem- C*HC 10.10800 284512.0 ; C1C2 10.16020 292880.0 ; C2C3 10.16020 292880.0 ; I am not sure to put C C or C1 C2 here; I tried both, neither worked. [ angletypes ] ; ijk func th0 cth HW OW HW 1 109.500627.600 ; For TIP4F Water - wj 1/98 HW OW LP 154.750418.400 ; For TIP4F Water - wj 1/98 OU U OU 1 180.000 1255.200 ; J Phys Chem 97, 5685 (1993) HC C* CW 1 126.800292.880 ; HC C* CB 1 126.800292.880 ; HC CS CW 1 126.800292.880 ; However, the parameters that we had in topol file are different: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 5 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 5 1 2 1 6 1 5 1 6 1 How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the ffbonded.itp? It looks them up from ffbonded.itp. You have a bond between atoms 1 and 2. Atoms 1 and 2 have assigned types, per the [atoms] directive. grompp goes into ffbonded.itp and looks for a bond between the types corresponding to that set of atoms. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] deformation in cnt
On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Justin Based on your suggestion, I added C-C bond length to z dimension of box (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). Then I used genion to neutralize system using replacing 2 water molecules by 2 Na ions, gro file obtained from genion is strange. When I see this gro file by vmd, some carbon atoms of CNT leave the box. Figure is in the bellow link: https://www.dropbox.com/s/kt1xk4ps3kbxze3/cnt-pic.docx What is reason of this issue? How to fix it? Looks like normal PBC, but possibly poor input geometry. Does energy minimization lead to a (visually) better state? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Strange trjconv error
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I then generated
a .tpr using grompp
When I do any simple gromacs command like:
trjconv -f 130ns-141ns.pdb -s ref.tpr -o 130ns-141ns.xtc
I get the following error:
Fatal error:
An input file contains a line longer than 4096 characters, while the buffer
passed to fgets2 has size 4096. The line starts with: '20s'
wc -L ref.tpr
20344 ref.tpr
The gmxdump of the .tpr along with grep gave me the offending line. It is
essentially the protein description:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01,
q=-6.0e-01, mB= 1.40067e+01, qB=-6.0e-01, resind=0, atomnumber=
-1}
atom[ 1]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-1.0e-01, mB= 1.20107e+01, qB=-1.0e-01, resind=
0, atomnumber= -1}
atom[ 2]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 3]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 4]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber=
-1}...
Any idea about how to proceed. I am quite stumped.
Thanks.
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Strange trjconv error
On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.comwrote:
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I then generated
a .tpr using grompp
When I do any simple gromacs command like:
trjconv -f 130ns-141ns.pdb -s ref.tpr -o 130ns-141ns.xtc
I get the following error:
Fatal error:
An input file contains a line longer than 4096 characters, while the buffer
passed to fgets2 has size 4096. The line starts with: '20s'
Unfortunately this is an output bug, so the '20s' is not actually useful to
you. Looks like something needs to be fixed in fgets2().
wc -L ref.tpr
20344 ref.tpr
The gmxdump of the .tpr along with grep gave me the offending line. It is
essentially the protein description:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01,
q=-6.0e-01, mB= 1.40067e+01, qB=-6.0e-01, resind=0, atomnumber=
-1}
atom[ 1]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-1.0e-01, mB= 1.20107e+01, qB=-1.0e-01, resind=
0, atomnumber= -1}
atom[ 2]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 3]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 4]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber=
-1}...
Any idea about how to proceed. I am quite stumped.
The problem is not in the .tpr file, it is in the .pdb file. Something
about its format is bad. Why not use catdcd to produce a .trr file instead?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
[gmx-users] Computing the energy of interaction
I have a paracetamol crystal and I would like to estimate the paracetamol/paracetamol energy of interaction per unitcell. To do this I am doing the following: Energy of interaction of paracetamols per unitcell= Total energy of a unitcell - (Energy of a molecule in the unitcell* number of the molecules in the unitcell) Energy of interaction of paracetamols per unitcell= Term1 + Term2 How to compute Term1: Took a crystal slab. Compute the total energy(using steepest decent) and divide it by the number of unitcells. The results is: -2443.29 kj/mol How to compute Term2: number of the molecules in the unitcell is 4. Energy of a single molecule in vacuum is 490.20 kj/mol Therefore: Energy of interaction of paracetamols per unitcell= -2443.29 kj/mol-(-490.20*4) kj/mol= -482.378 kj/mol Which is more than a covalent bond! Could you please help me to figure out what is going wrong? Thanks G. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] constraining protein in the box
On Tue, Dec 10, 2013 at 12:31 PM, Shine A shin...@iisertvm.ac.in wrote: Sir, I completed a 400 ns MD simulation. But in some part of the trajectory my protein is just out side the box I selected (triclinic). Is there any option in gromacs to constrain my protein in box during simulation. No, nor is there any need to do so because there is no such thing as inside or outside of an infinite system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ligand covalently bond with the protein
Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ligand covalently bond with the protein
On Tue, Dec 10, 2013 at 7:28 PM, aixintiankong aixintiank...@126.comwrote: Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! Please refer to the link I posted before. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-December/086116.html -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Strange trjconv error
Dear Justin,
Thanks for the suggestion.
Producing a .trr in catdcd still failed because it apparently produces a
trajectory without a timestamp. So, I loaded the .dcd into vmd and saved
the coordinates in a .trr file. This worked like a charm :)
Note to self: Install gromacs with the vmd plugin next time...
On Tue, Dec 10, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I then
generated
a .tpr using grompp
When I do any simple gromacs command like:
trjconv -f 130ns-141ns.pdb -s ref.tpr -o 130ns-141ns.xtc
I get the following error:
Fatal error:
An input file contains a line longer than 4096 characters, while the
buffer
passed to fgets2 has size 4096. The line starts with: '20s'
Unfortunately this is an output bug, so the '20s' is not actually useful to
you. Looks like something needs to be fixed in fgets2().
wc -L ref.tpr
20344 ref.tpr
The gmxdump of the .tpr along with grep gave me the offending line. It is
essentially the protein description:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01,
q=-6.0e-01, mB= 1.40067e+01, qB=-6.0e-01, resind=0,
atomnumber=
-1}
atom[ 1]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-1.0e-01, mB= 1.20107e+01, qB=-1.0e-01, resind=
0, atomnumber= -1}
atom[ 2]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 3]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 4]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber=
-1}...
Any idea about how to proceed. I am quite stumped.
The problem is not in the .tpr file, it is in the .pdb file. Something
about its format is bad. Why not use catdcd to produce a .trr file
instead?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
